Pureblood rely on fabricants to work for them as they have forget how. Why would Unanimity sic purebloods on fabricants for just a cover up and inevitably dooms everyone?
Unanimity was hoping that by causing purebloods to hate fabricants even more that even the moderate anti-slavery movement would be abolished and that there would be even more control over the fabricants and purebloods.
Perhaps not so much a headscratcher, but does Sonmi's genetic line survive to the events in Sloosha's Crossin' an' Ev'rythin' After and beyond? Do any escape Earth to the off-world colonies? The film does not give any direct clues as to whether the Sonmi-451's and Yoona-939s line survives, or any of the other fabricants. Is it possible that Zachrys sister Rose is directly descended from a fabricant herself?
The book implies that there was some kind fabricant revolution along with pureblood nuclear wars, and some descriptions of the slightly mutated looking humans might imply that fabricants found a way to reproduce and mixed with pureblood humans.